6CI5 | pdb_00006ci5

Crystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis in complex with UDP-4,6-dideoxy-4-formamido-L-AltNAc and tetrahydrofolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain.

Reimer, J.M.Harb, I.Ovchinnikova, O.G.Jiang, J.Whitfield, C.Schmeing, T.M.

(2018) ACS Chem Biol 13: 3161-3172

  • DOI: https://doi.org/10.1021/acschembio.8b00739
  • Primary Citation Related Structures: 
    6CI2, 6CI4, 6CI5, 6EDK

  • PubMed Abstract: 

    Nonribosomal peptide synthetases (NRPSs) increase the chemical diversity of their products by acquiring tailoring domains. Linear gramicidin synthetase starts with a tailoring formylation (F) domain, which likely originated from a sugar formyltransferase (FT) gene. Here, we present studies on an Anoxybacillus kamchatkensis sugar FT representative of the prehorizontal gene transfer FT. Gene cluster analysis reveals that this FT acts on a UDP-sugar in a novel pathway for synthesis of a 7-formamido derivative of CMP-pseudaminic acid. We recapitulate the pathway up to and including the formylation step in vitro, experimentally demonstrating the role of the FT. We also present X-ray crystal structures of the FT alone and with ligands, which unveil contrasts with other structurally characterized sugar FTs and show close structural similarity with the F domain. The structures reveal insights into the adaptations that were needed to co-opt and evolve a sugar FT into a functional and useful NRPS domain.


  • Organizational Affiliation
    • Department of Biochemistry , McGill University , Montréal , Québec H3G 0B1 , Canada.

Macromolecule Content 

  • Total Structure Weight: 26.77 kDa 
  • Atom Count: 1,670 
  • Modeled Residue Count: 189 
  • Deposited Residue Count: 217 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
formyltransferase PseJ217Anoxybacillus ayderensis G10Mutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F5G

Query on F5G



Download:Ideal Coordinates CCD File
C [auth A](2R,3R,4S,5R,6S)-3-(acetylamino)-5-(formylamino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
C18 H28 N4 O16 P2
MNNFOPXYMSSSNV-XQDVVILDSA-N
1YJ

Query on 1YJ



Download:Ideal Coordinates CCD File
D [auth A]N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
C19 H23 N7 O6
MSTNYGQPCMXVAQ-NEPJUHHUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.42α = 90
b = 73.78β = 103.47
c = 41.8γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN-148472

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description